great question;
Momir Farooq made a lot of card templates and tokens I use, thank you Momir Farooq
though Galak Fyyar, SquelchDog, CerousMutor and Surf have also made hi-res stuff,
and some of the images are available directly from DevArt as ready to use gifs etc,
I hope that gives you a lot of options

then, there's the free-personal use images from Star Wars Wikia, wookiepedia,
which helps enormously for the images.
They're very high-res simple linearts which'll do the job.

The Separatists are relatively easy to make a logo for,
it's a hexagon inside a hexagon with cantons of trapeziums

turning to tokens themselves,
Momir Farooq and Warev Ririp have made frankly, AWESOME tokens as a 2D disc/coin
and as a 2d-3D stand-in for proxy armies - a great gateway to pepakura for new people to the game,
or for those with no access to minis.

If you're wanting something more like the tokens that
come in FFG's Imperial Assault, or SW:Xwing etc,
you can take your designs to a local printers, and get it printed on 280GSM dull-gloss cardstock.
that will be a screen-print stuck to the card, and punch-cut.

If you want to get really fancy,
some folks quest for 'mission coins',
I saw once a game of Star Wars Minis, and the tournament winner won a custom faction-specific 'mission coin',
it was custom made by a trophy-maker, and it looked awesome from pewter and electro-plated 'german silver'.
it had acid-etched reliefs, which made the faction symbol 'shimmer' in that rainbowed or 'blued' metal finish.
I've also seen custom 'republic credits' replete with aurekbesh, made by Franklin Mint, in troy-ounce platinum. Good luck hunting those pretties
There are several 'artists' on DevArt who would handle such a thing.

I hope this was of some use for you,
and gave you some options
Hopefully people with the answers post soon, if not...
there may also be a thread on BoardGameGeek

Good hunting,
and you'll have to share whatever you come up with on the customs thread.